A CDC microbiologist holds a plate demonstrating the modified Hodge test, which is used to identify resistant Enterobacteriaceae.

One of the most urgent antibiotic resistance threats may be even more crafty and capable of spreading than suspected, according to a new study.

The research, published yesterday in the Proceedings of the National Academy of Sciences, indicates that carbapenem-resistant Enterobacteriaceae (CRE), a family of bacteria that are resistant to several classes of antibiotics and can cause severe and sometimes deadly infections, are more diverse, have more resistance mechanisms, and are more capable of increasing the spread of resistance than previously thought. And while CRE are known for causing outbreaks in hospitals, the study suggests they may be able to fly under the radar in both community and healthcare settings.

Greater diversity of species, resistance mechanisms

For the study, researchers collected and genetically sequenced more than 250 CRE isolates that caused disease in three hospitals in the Boston area and one hospital in Irvine, California, over a 16-month period in 2012 and 2013. The isolates came from patient blood, wound, respiratory tract, and urine samples.

The aim, the authors of the study wrote, was to get a "snapshot" of the genetic diversity of CREs both within and among hospitals and determine how the bugs were spreading.

Overall, eight species of CRE were found at the four hospitals, with the majority being Klebsiella pneumoniae of the sequence type 258 (ST258) lineage, which is responsible for much of the rise in CRE incidence in the United States, the authors explain. Escherichia coli and Enterobacter cloacae were the other resistant species most commonly found among the isolates.

The number of CRE species identified surprised the authors, as did the fact that few of the isolates appeared to be genetically related. Those findings suggest that most were not linked to a hospital outbreak in which a CRE infection was spreading from patient to patient.

What also surprised them was the amount of diversity they found in terms of resistance mechanisms. K pneumoniae CRE strains often carry genes encoded with carbapenemases—enzymes that break down carbapenem antibiotics—on highly mobile plasmids that can be easily passed along to other K pneumonia strains and other species of bacteria, such as E coli. Carbapenems are a last-resort antibiotic that are essential for treating multidrug-resistant infections.

Although they aren't the only type of enzyme that can break down carbapenems, K pneumoniae carbapenemases (KPCs) are the most common found in CRE samples in the United States, and they are believed to be the major driver of carbapenem resistance.

While KPC-encoded genes were identified in many of the isolates, so were other known resistance genes. Furthermore, in some of the isolates, the researchers could not identify the gene responsible for carbapenem resistance. And that's a cause for concern, they say.

"Although not all mechanisms have been revealed, the fact that these unexplained mechanisms of CRE exist is a critical result and shows that there are many ways to achieve carbapenem resistance and that we should be vigilant as new ones emerge," the authors wrote.

In addition, the authors identified several different types of plasmids responsible for sharing resistance genes with other strains and species of bacteria. These mobile pieces of DNA are the reason why CRE infections so easily spread within hospital settings.

'Unobserved transmission'

CRE are already high on the list of drug-resistant bacteria that concern public health officials. The Centers for Disease Control and Prevention estimates that more than 9,000 healthcare-associated CRE infections occur each year in the United States, and that CRE bloodstream infections kill up to half the people who get them. Agency labs have confirmed at least one type of CRE in healthcare facilities in 44 states. Last week, the agency published a report on a Nevada woman who died of a K pneumoniae CRE infection that was resistant to all available antibiotics.

But CRE infections tend to be found among critically ill patients in acute care hospitals and long-term healthcare facilities, and that's where surveillance is focused. What concerns senior study author William Hanage, PhD, about these findings is that they suggest some patients may be carrying CRE asymptomatically at other points in the continuum of care where physicians aren't looking for it, and it could be spreading silently.

"While the typical focus has been on treating sick patients with CRE-related infections, our new findings suggest that CRE is spreading beyond the obvious cases of disease. We need to look harder for this unobserved transmission within our communities and healthcare facilities if we want to stamp it out," Hanage said in a press release from Harvard T.H. Chan School of Public Health, where he's an associate professor of epidemiology.

What will make that difficult, Harange and his colleagues noted, is that current diagnostic tests look for certain genetic culprits to detect CRE, like the KPC gene. That means clinicians could miss a significant number of CRE infections. They say whole genome–based surveillance studies are needed to better define the scope of the CRE problem.